Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005050.1 Corchorus capsularis cultivar CVL-1 contig05068, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20960
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Found at i:771 original size:11 final size:11
Alignment explanation
Indices: 728--765 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
718 TTCCTATATA
*
728 AAATAAATTAT
1 AAATTAATTAT
739 CAAA-TAATTAT
1 -AAATTAATTAT
750 AAATTAATTAT
1 AAATTAATTAT
761 AAATT
1 AAATT
766 TGTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:1150 original size:48 final size:48
Alignment explanation
Indices: 1079--1171 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
1069 ACAAAATTTT
1079 ATTTCTTAATTGAATTTTCTTAAAAGAATTTATAAAATAAAACAGTTC
1 ATTTCTTAATTGAATTTTCTTAAAAGAATTTATAAAATAAAACAGTTC
*
1127 ATTTCTTAATTGAATTTTTTTAAAAGAATTTATAAAATAAAACAG
1 ATTTCTTAATTGAATTTTCTTAAAAGAATTTATAAAATAAAACAG
1172 CCGCACGCGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (48 bp):
ATTTCTTAATTGAATTTTCTTAAAAGAATTTATAAAATAAAACAGTTC
Found at i:2891 original size:107 final size:107
Alignment explanation
Indices: 2658--2884 Score: 337
Period size: 107 Copynumber: 2.1 Consensus size: 107
2648 GTTATATATC
* * * **
2658 TTATTTATAAAACCTTATAACAATATATTATTAATTATGCAATTTACACTTAAAATAAAAATAAA
1 TTATTTCTAAAACCATATAACAATAAATTATTAATTATAAAATTTACACTTAAAATAAAAATAAA
* * * * *
2723 ATTTTAATTTGGGGTTAAACTTAGTTAAATTAGTTTTGTATT
66 ATTTTAATTTGGGGCTAAACTTAGTGAAATCAGTTTTATACT
* * *
2765 TTATTTCTAAAACCATATAACAATAAATTATTAATTTTAAAATTTACCCTTAGAATAAAAATAAA
1 TTATTTCTAAAACCATATAACAATAAATTATTAATTATAAAATTTACACTTAAAATAAAAATAAA
2830 ATTTTAATTTGGGGCTAAACTTAGTGAAATCAGTTTTATACT
66 ATTTTAATTTGGGGCTAAACTTAGTGAAATCAGTTTTATACT
2872 TTATTTCTAAAAC
1 TTATTTCTAAAAC
2885 TCTATAATAA
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (107 bp):
TTATTTCTAAAACCATATAACAATAAATTATTAATTATAAAATTTACACTTAAAATAAAAATAAA
ATTTTAATTTGGGGCTAAACTTAGTGAAATCAGTTTTATACT
Found at i:2906 original size:107 final size:107
Alignment explanation
Indices: 2658--2926 Score: 308
Period size: 107 Copynumber: 2.5 Consensus size: 107
2648 GTTATATATC
* * * * * * **
2658 TTATTTATAAAACCTTATAACAATATATTATTAATTATGCAATTTACACTTAAAATAAAAATAAA
1 TTATTTCTAAAACCATATAACAAAAAACTATTAATTTTAAAATTTACACTTAAAATAAAAATAAA
* * * * *
2723 ATTTTAATTTGGGGTTAAACTTAGTTAAATTAGTTTTGTATT
66 ATTTTAATTTGGGGCTAAACTTAGTGAAATCAGTTTTATACT
* * * *
2765 TTATTTCTAAAACCATATAACAATAAATTATTAATTTTAAAATTTACCCTTAGAATAAAAATAAA
1 TTATTTCTAAAACCATATAACAAAAAACTATTAATTTTAAAATTTACACTTAAAATAAAAATAAA
2830 ATTTTAATTTGGGGCTAAACTTAGTGAAATCAGTTTTATACT
66 ATTTTAATTTGGGGCTAAACTTAGTGAAATCAGTTTTATACT
* ** * *
2872 TTATTTCTAAAACTC-TATAATAAAAAACCT-TTAATTGCATAATTTACTCTTAAAA
1 TTATTTCTAAAAC-CATATAACAAAAAA-CTATTAATTTTAAAATTTACACTTAAAA
2927 ATTAAATTTA
Statistics
Matches: 139, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
107 137 0.99
108 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (107 bp):
TTATTTCTAAAACCATATAACAAAAAACTATTAATTTTAAAATTTACACTTAAAATAAAAATAAA
ATTTTAATTTGGGGCTAAACTTAGTGAAATCAGTTTTATACT
Found at i:3558 original size:25 final size:25
Alignment explanation
Indices: 3524--3572 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
3514 AATCAGTAAT
*
3524 AATCAATCAATAATTATTTACTTTC
1 AATCAATCAATAATGATTTACTTTC
3549 AATCAATCAATAATGATTTACTTT
1 AATCAATCAATAATGATTTACTTT
3573 AAATAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (25 bp):
AATCAATCAATAATGATTTACTTTC
Found at i:14998 original size:3 final size:3
Alignment explanation
Indices: 14992--15019 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
14982 GATGAAGATG
14992 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
15020 GGAAGAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:15342 original size:28 final size:29
Alignment explanation
Indices: 15310--15403 Score: 82
Period size: 28 Copynumber: 3.6 Consensus size: 29
15300 CTCGGATTGG
15310 GAAGTTCAG-GGGCAAAATGTCCTGATTT
1 GAAGTTCAGAGGGCAAAATGTCCTGATTT
* * *
15338 GAAGTTTAGAGGGC-AAACG--C--A-AT
1 GAAGTTCAGAGGGCAAAATGTCCTGATTT
15361 --AGTTCAG-GGGCAAAATGTCCTGATTT
1 GAAGTTCAGAGGGCAAAATGTCCTGATTT
*
15387 GAAGTTTAGAGGGCAAA
1 GAAGTTCAGAGGGCAAA
15404 CGCAAAAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 19
0.65 0.09 0.25
Matches are distributed among these distances:
20 4 0.08
21 10 0.20
23 2 0.04
24 1 0.02
25 1 0.02
26 2 0.04
28 18 0.37
29 11 0.22
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (29 bp):
GAAGTTCAGAGGGCAAAATGTCCTGATTT
Found at i:15384 original size:49 final size:49
Alignment explanation
Indices: 15312--15408 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
15302 CGGATTGGGA
15312 AGTTCAGGGGCAAAATGTCCTGATTTGAAGTTTAGAGGGCAAACGCAAT
1 AGTTCAGGGGCAAAATGTCCTGATTTGAAGTTTAGAGGGCAAACGCAAT
15361 AGTTCAGGGGCAAAATGTCCTGATTTGAAGTTTAGAGGGCAAACGCAA
1 AGTTCAGGGGCAAAATGTCCTGATTTGAAGTTTAGAGGGCAAACGCAA
15409 AAAAGGCTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (49 bp):
AGTTCAGGGGCAAAATGTCCTGATTTGAAGTTTAGAGGGCAAACGCAAT
Found at i:20741 original size:21 final size:21
Alignment explanation
Indices: 20715--20759 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20705 AAAATCTGGA
*
20715 TTGCTAAACACCGTCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
20736 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
20757 TTG
1 TTG
20760 ACGTCTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Done.